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- EMDB-36791: SID1 transmembrane family member 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-36791
TitleSID1 transmembrane family member 1
Map data
Sample
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / TRANSPORT PROTEIN
Function / homologyRNA transmembrane transporter activity / SID1 transmembrane family / dsRNA-gated channel SID-1 / RNA transport / cholesterol binding / double-stranded RNA binding / lysosome / plasma membrane / SID1 transmembrane family member 1
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsGuo H / Qi C / Lu Y / Yang H / Zhu Y / Sun F / Ji X
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Cell Res / Year: 2024
Title: Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity.
Authors: Le Zheng / Tingting Yang / Hangtian Guo / Chen Qi / Yuchi Lu / Haonan Xiao / Yan Gao / Yue Liu / Yixuan Yang / Mengru Zhou / Henry C Nguyen / Yun Zhu / Fei Sun / Chen-Yu Zhang / Xiaoyun Ji /
History
DepositionJul 10, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36791.png

Downloads & links

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Map

FileDownload / File: emd_36791.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 164 pix.
= 221.4 Å		1.35 Å/pix.
x 164 pix.
= 221.4 Å		1.35 Å/pix.
x 164 pix.
= 221.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.0996943 - 4.4586477
Average (Standard dev.)0.0070103887 (±0.12071278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 221.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36791_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36791_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD f...

EntireName: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement
Components
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD f...

SupramoleculeName: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SID1 transmembrane family member 1

MacromoleculeName: SID1 transmembrane family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.089018 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DFDHVYSGVV NLSTENIYSF NYTSQPDQVT AVRVYVNSSS ENLNYPVLVV VRQQKEVLSW QVPLLFQGLY QRSYNYQEVS RTLCPSEAT NETGPLQQLI FVDVASMAPL GAQYKLLVTK LKHFQLRTNV AFHFTASPSQ PQYFLYKFPK DVDSVIIKVV S EMAYPCSV ...String:
DFDHVYSGVV NLSTENIYSF NYTSQPDQVT AVRVYVNSSS ENLNYPVLVV VRQQKEVLSW QVPLLFQGLY QRSYNYQEVS RTLCPSEAT NETGPLQQLI FVDVASMAPL GAQYKLLVTK LKHFQLRTNV AFHFTASPSQ PQYFLYKFPK DVDSVIIKVV S EMAYPCSV VSVQNIMCPV YDLDHNVEFN GVYQSMTKKA AITLQKKDFP GEQFFVVFVI KPEDYACGGS FFIQEKENQT WN LQRKKNL EVTIVPS

UniProtKB: SID1 transmembrane family member 1

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94868
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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